Imaging
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Virtual screening for small-molecule pathway regulators by image-profile matching. Cell Syst. 2022. doi:10.1016/j.cels.2022.08.003.
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A New Image for Cell Sorting. N Engl J Med. 2022;386(18):1755-1758. doi:10.1056/NEJMcibr2200971. .
Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic. PLoS Comput Biol. 2022;18(2):e1009888. doi:10.1371/journal.pcbi.1009888. .
The new era of quantitative cell imaging-challenges and opportunities. Mol Cell. 2022;82(2):241-247. doi:10.1016/j.molcel.2021.12.024. .
In vitro neutrophil migration is associated with inhaled corticosteroid treatment and serum cytokines in pediatric asthma. Front Pharmacol. 2022;13:1021317. doi:10.3389/fphar.2022.1021317.
2020 BioImage Analysis Survey: Community experiences and needs for the future. Biol Imaging. 2022;1. doi:10.1017/S2633903X21000039. .
A Multiparametric Activity Profiling Platform for Neuron Disease Phenotyping and Drug Screening. Mol Biol Cell. 2021:mbcE21100481. doi:10.1091/mbc.E21-10-0481.
A field guide to cultivating computational biology. PLoS Biol. 2021;19(10):e3001419. doi:10.1371/journal.pbio.3001419.
CellProfiler 4: improvements in speed, utility and usability. BMC Bioinformatics. 2021;22(1):433. doi:10.1186/s12859-021-04344-9. .
CellProfiler Analyst 3.0: Accessible data exploration and machine learning for image analysis. Bioinformatics. 2021. doi:10.1093/bioinformatics/btab634. .
Genes in human obesity loci are causal obesity genes in C. elegans. PLoS Genet. 2021;17(9):e1009736. doi:10.1371/journal.pgen.1009736.
Inter-laboratory automation of the in vitro micronucleus assay using imaging flow cytometry and deep learning. Arch Toxicol. 2021;95(9):3101-3115. doi:10.1007/s00204-021-03113-0.
Deepometry, a framework for applying supervised and weakly supervised deep learning to imaging cytometry. Nat Protoc. 2021;16(7):3572-3595. doi:10.1038/s41596-021-00549-7.
Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging. Commun Biol. 2021;4(1):786. doi:10.1038/s42003-021-02276-x.
Which image-based phenotypes are most promising for using AI to understand cellular functions and why?. Cell Syst. 2021;12(5):384-387. doi:10.1016/j.cels.2021.04.012.
ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis. Curr Protoc. 2021;1(5):e89. doi:10.1002/cpz1.89. .
Developing open-source software for bioimage analysis: opportunities and challenges. F1000Res. 2021;10:302. doi:10.12688/f1000research.52531.1. .
TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41. Cell Rep. 2020;33(6):108371. doi:10.1016/j.celrep.2020.108371.
Diagnostic Potential of Imaging Flow Cytometry. Trends Biotechnol. 2018;36(7):649-652. doi:10.1016/j.tibtech.2017.12.008.
CellProfiler 3.0: Next-generation image processing for biology. PLoS Biol. 2018;16(7):e2005970. doi:10.1371/journal.pbio.2005970.
Repurposing High-Throughput Image Assays Enables Biological Activity Prediction for Drug Discovery. Cell Chem Biol. 2018;25(5):611-618.e3. doi:10.1016/j.chembiol.2018.01.015.
Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface. 2018;15(141). doi:10.1098/rsif.2017.0387.
Combining morphological and migration profiles of in vitro time-lapse data. In: IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018). IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018).; Submitted. .
Quality Control for High-Throughput Imaging Experiments Using Machine Learning in Cellprofiler. Methods Mol Biol. 2018;1683:89-112. doi:10.1007/978-1-4939-7357-6_7. .
Designed Surface Topographies Control ICAM-1 Expression in Tonsil-Derived Human Stromal Cells. Front Bioeng Biotechnol. 2018;6:87. doi:10.3389/fbioe.2018.00087.
A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay. Gigascience. 2017;6(12):1-5. doi:10.1093/gigascience/giw014.
Reconstructing cell cycle and disease progression using deep learning. Nat Commun. 2017;8(1):463. doi:10.1038/s41467-017-00623-3.
Data-analysis strategies for image-based cell profiling. Nat Methods. 2017;14(9):849-863. doi:10.1038/nmeth.4397.
Mining for osteogenic surface topographies: In silico design to in vivo osseo-integration. Biomaterials. 2017;137:49-60. doi:10.1016/j.biomaterials.2017.05.020.
Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence. PLoS Pathog. 2017;13(5):e1006363. doi:10.1371/journal.ppat.1006363.
Systematic morphological profiling of human gene and allele function via Cell Painting. Elife. 2017;6. doi:10.7554/eLife.24060.
Applying Faster R-CNN for Object Detection on Malaria Images. . In: 2017 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW). 2017 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW).; Submitted.
CytoGAN: Generative Modeling of Cell Images. In: Workshop on Machine Learning in Computational Biology, Neural Information Processing Systems. . Workshop on Machine Learning in Computational Biology, Neural Information Processing Systems. .; Submitted. doi:https://doi.org/10.1101/227645. .
An open-source solution for advanced imaging flow cytometry data analysis using machine learning. Methods. 2017;112:201-210. doi:10.1016/j.ymeth.2016.08.018.
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Imagining the future of bioimage analysis. Nat Biotechnol. 2016;34(12):1250-1255. doi:10.1038/nbt.3722. .
High-Throughput Platform for Identifying Molecular Factors Involved in Phenotypic Stabilization of Primary Human Hepatocytes In Vitro. J Biomol Screen. 2016;21(9):897-911. doi:10.1177/1087057116660277. .
Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nat Protoc. 2016;11(9):1757-74. doi:10.1038/nprot.2016.105.
QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni. J Chem Inf Model. 2016;56(7):1357-72. doi:10.1021/acs.jcim.6b00055.
CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets. Bioinformatics. 2016. doi:10.1093/bioinformatics/btw390. .
An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells. Exp Eye Res. 2016;147:50-6. doi:10.1016/j.exer.2016.04.012.
Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification. Methods. 2016;96:6-11. doi:10.1016/j.ymeth.2015.12.002. .
CP-CHARM: segmentation-free image classification made accessible. BMC Bioinformatics. 2016;17:51. doi:10.1186/s12859-016-0895-y. .
A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells. Cell Rep. 2016;14(3):611-20. doi:10.1016/j.celrep.2015.12.051.
Label-free cell cycle analysis for high-throughput imaging flow cytometry. Nat Commun. 2016;7:10256. doi:10.1038/ncomms10256.
CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data. BMC Bioinformatics. 2015;16:368. doi:10.1186/s12859-015-0759-x. .
CDy6, a photostable probe for long-term real-time visualization of mitosis and proliferating cells. Chem Biol. 2015;22(2):299-307. doi:10.1016/j.chembiol.2014.11.018.
Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images. Curr Protoc Mol Biol. 2015;109:14.17.1-13. doi:10.1002/0471142727.mb1417s109. .
Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects. PLoS One. 2015;10(7):e0131370. doi:10.1371/journal.pone.0131370.
Crowdsourcing the creation of image segmentation algorithms for connectomics. Front Neuroanat. 2015;9:142. doi:10.3389/fnana.2015.00142.
ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments. Bioinformatics. 2014;30(23):3440-2. doi:10.1093/bioinformatics/btu554.
Pipeline for illumination correction of images for high-throughput microscopy. J Microsc. 2014;256(3):231-6. doi:10.1111/jmi.12178. .
Nanoparticle vesicle encoding for imaging and tracking cell populations. Nat Methods. 2014;11(11):1177-81. doi:10.1038/nmeth.3105.
High- and low-throughput scoring of fat mass and body fat distribution in C. elegans. Methods. 2014;68(3):492-9. doi:10.1016/j.ymeth.2014.04.017.
Increasing the Content of High-Content Screening: An Overview. J Biomol Screen. 2014;19(5):640-50. doi:10.1177/1087057114528537. .
Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth. PLoS Pathog. 2014;10(2):e1003946. doi:10.1371/journal.ppat.1003946.
ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state. Cell Rep. 2014;6(2):313-24. doi:10.1016/j.celrep.2013.12.032.
High content image analysis identifies novel regulators of synaptogenesis in a high-throughput RNAi screen of primary neurons. PLoS One. 2014;9(3):e91744. doi:10.1371/journal.pone.0091744.
Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment. J Biomol Screen. 2013;18(10):1321-9. doi:10.1177/1087057113503553.
Niche-based screening identifies small-molecule inhibitors of leukemia stem cells. Nat Chem Biol. 2013;9(12):840-848. doi:10.1038/nchembio.1367.
Identification of small molecules for human hepatocyte expansion and iPS differentiation. Nat Chem Biol. 2013;9(8):514-20. doi:10.1038/nchembio.1270.
A microscale human liver platform that supports the hepatic stages of Plasmodium falciparum and vivax. Cell Host Microbe. 2013;14(1):104-15. doi:10.1016/j.chom.2013.06.005.
Multiplex cytological profiling assay to measure diverse cellular states. PLoS One. 2013;8(12):e80999. doi:10.1371/journal.pone.0080999.
Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL.
Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL. Cell. 2012;150(3):575-89. doi:10.1016/j.cell.2012.06.032.
Annotated high-throughput microscopy image sets for validation. Nat Methods. 2012;9(7):637. doi:10.1038/nmeth.2083. .
A call for bioimaging software usability. Nat Methods. 2012;9(7):666-70. doi:10.1038/nmeth.2073. .
An image analysis toolbox for high-throughput C. elegans assays. Nat Methods. 2012;9(7):714-6. doi:10.1038/nmeth.1984.
Workflow and metrics for image quality control in large-scale high-content screens. J Biomol Screen. 2012;17(2):266-74. doi:10.1177/1087057111420292. .
A chemical screen probing the relationship between mitochondrial content and cell size. PLoS One. 2012;7(3):e33755. doi:10.1371/journal.pone.0033755.
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Human tumors instigate granulin-expressing hematopoietic cells that promote malignancy by activating stromal fibroblasts in mice. J Clin Invest. 2011;121(2):784-99. doi:10.1172/JCI43757.
Screening cellular feature measurements for image-based assay development. J Biomol Screen. 2010;15(7):840-6. doi:10.1177/1087057110370895. .
Introduction to the quantitative analysis of two-dimensional fluorescence microscopy images for cell-based screening. PLoS Comput Biol. 2009;5(12):e1000603. doi:10.1371/journal.pcbi.1000603. .
Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution. Bioinformatics. 2009;25(8):1078-9. doi:10.1093/bioinformatics/btp091. .
Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. Proc Natl Acad Sci U S A. 2009;106(6):1826-31. doi:10.1073/pnas.0808843106.
Extracting rich information from images. Methods Mol Biol. 2009;486:193-211. doi:10.1007/978-1-60327-545-3_14. .
CellProfiler Analyst: data exploration and analysis software for complex image-based screens. BMC Bioinformatics. 2008;9:482. doi:10.1186/1471-2105-9-482.
High-throughput screens for fluorescent dye discovery. Trends Biotechnol. 2008;26(10):527-30. doi:10.1016/j.tibtech.2008.06.008. .
Image-based chemical screening. Nat Chem Biol. 2007;3(8):461-5. doi:10.1038/nchembio.2007.15. .